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Proteomic analysis of the secretome of Leishmania donovani

J Maxwell Silverman123, Simon K Chan456, Dale P Robinson27, Dennis M Dwyer6, Devki Nandan12, Leonard J Foster27 and Neil E Reiner123*

Author Affiliations

1 Department of Medicine (Division of Infectious Diseases), University of British Columbia, Faculty of Medicine, 2733 Heather St, Vancouver, British Columbia, V5Z 3J5, Canada

2 Vancouver Coastal Health Research Institute, 2647 Willow St. Vancouver, British Columbia, V5Z 3P1, Canada

3 Department Microbiology and Immunology, University of British Columbia, Faculty of Science, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada

4 Canada's Michael Smith Genome Sciences Centre, 570 West 7th Ave - Suite 100, Vancouver, British Columbia, V5Z 4S6, Canada

5 Bioinformatics Graduate Program, University of British Columbia, 100-570 West 7th Avenue, Vancouver, British Columbia, V5Z 4S6 Canada

6 Laboratory of Parasitic Diseases, Division of Intramural Research, NIAID, National Institutes of Health, 4 Center Drive, Bethesda, Maryland, 20892, USA

7 Department of Biochemistry and Molecular Biology, University of British Columbia, Faculty of Science, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada

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Genome Biology 2008, 9:R35  doi:10.1186/gb-2008-9-2-r35

Published: 18 February 2008

Additional files

Additional data file 1:

358 proteins had at least two nonoverlapping peptides that were detected and quantified in three or more individual analyses of leishmania Cm proteins. The peptides corresponding to each identification are shown. Protein identities were determined as described in Materials and methods and for Tables 1 to 3.

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Additional data file 2:

After determining which proteins were to be considered for analysis (as described in Materials and methods and for Additional Data File 1), the measured Cm/CA ratios were normalized to the measured value of histone H2B in each independent experiment. The normalized values were then log normal (Ln) transformed (mean Ln transformed Cm/CA ratio, experiments [Exps] 1 to 4) to reduce the spread of the data. The means of the Ln transformed ratios for each protein identity were then calculated (mean Ln transformed values). The relative standard deviations of the peptide ratios for each analysis are included.

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Additional data file 3:

GO annotation of the proteins detected in leishmania Cm. *Proteins with amino-terminal secretion signal peptides, and proteins shown to be antigenic. GO IDs lists the GO identification number associated with each protein, and GO Term lists the term associated with each GO ID. C, cellular compartment; F, molecular function; P, biologic process.

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Additional data file 4:

Leishmania proteins predicted to be classically secreted by a genome wide screen for proteins containing an amino-terminal secretion signal peptide. MS, proteins detected in the SILAC/mass spectrometry analysis; § proteins detected by mass spectrometry with ratios above the secretome cut-off; GPI, proteins found to contain a GPI attachment site; *, proteins previously reported to be secreted by leishmania.

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Additional data file 5:

Proteins with mean Cm/CA peptide ratios greater that two standard deviations above that of histone H2B were considered enriched. *Proteins with amino-terminal secretion signal peptides, and proteins shown to be antigenic. Microvesicle Association displays the vesicles associated with the protein ID. AP, adipocyte adiposome; BC, B-cell lymphocyte exosome; DC, dendritic cell exosome; Gly, glycosome.

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